I-TASSER results

I-TASSER results for job id Rv1126c

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Input Sequence in FASTA format

>protein (201 residues)
MSELTVLQAVRLKGRVITTDLAQTLGEDLADVAATVDRLTAAGLLVDATPLRISPSGRMR
LDDLLAEERNRADSTVLAAAYRDFRSVNADFKRLVTDWQLKGEKPNTHDDAEYDAAVLSR
LDGVHRRVGPIIGTVAMQLPRLSRYPVKLRAALDKVKAGDIAWLTRPLIDSYHTVWFELH
EELIQAVGLTRDEAAKSGDAQ

Predicted Secondary Structure

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSELTVLQAVRLKGRVITTDLAQTLGEDLADVAATVDRLTAAGLLVDATPLRISPSGRMRLDDLLAEERNRADSTVLAAAYRDFRSVNADFKRLVTDWQLKGEKPNTHDDAEYDAAVLSRLDGVHRRVGPIIGTVAMQLPRLSRYPVKLRAALDKVKAGDIAWLTRPLIDSYHTVWFELHEELIQAVGLTRDEAAKSGDAQ
Prediction	CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCHCCCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCC
Conf.Score	977899999998789999999999899999999999999998874446787579889999999999999975689999999987676599999999987688998877774556899999999999999999999986577888999999999999978867764577764567899999999999879766777756789
	H:Helix; S:Strand; C:Coil

Predicted Solvent Accessibility

Sequence	20 40 60 80 100 120 140 160 180 200 \| \| \| \| \| \| \| \| \| \| MSELTVLQAVRLKGRVITTDLAQTLGEDLADVAATVDRLTAAGLLVDATPLRISPSGRMRLDDLLAEERNRADSTVLAAAYRDFRSVNADFKRLVTDWQLKGEKPNTHDDAEYDAAVLSRLDGVHRRVGPIIGTVAMQLPRLSRYPVKLRAALDKVKAGDIAWLTRPLIDSYHTVWFELHEELIQAVGLTRDEAAKSGDAQ
Prediction	753030010020253053730242262447403520450254121344541402440354145214522652445203401640451154025003413356552453425622440154035015403510450052143044145204400530553335202413221002002100220032142526555644668
	Values range from 0 (buried residue) to 8 (highly exposed residue)

Predicted Normalized B-facotr

(B-factor is a value to indicate the extent of the inherent thermal mobility of residues/atoms in proteins. In I-TASSER, this value is deduced from threading template proteins from the PDB in combination with the sequence profiles derived from sequence databases. The reported B-factor profile in the figure below corresponds to the normalized B-factor of the target protein, defined by B=(B'-u)/s, where B' is the raw B-factor value, u and s are respectively the mean and standard deviation of the raw B-factors along the sequence. (Click here to read more about predicted normalized B-factor)

Top 10 threading templates used by I-TASSER

Rank

PDB
Hit

Iden1

Iden2

Cov

Norm.
Zscore

Download
Align.

                  20                  40                  60                  80                 100                 120                 140                 160                 180                 200

                   |                   |                   |                   |                   |                   |                   |                   |                   |                   |

Sec.Str
Seq

CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCHCCCCCCCCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCCCHHHCHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHCCCC
MSELTVLQAVRLKGRVITTDLAQTLGEDLADVAATVDRLTAAGLLVDATPLRISPSGRMRLDDLLAEERNRADSTVLAAAYRDFRSVNADFKRLVTDWQLKGEKPNTHDDAEYDAAVLSRLDGVHRRVGPIIGTVAMQLPRLSRYPVKLRAALDKVKAGDIAWLTRPLIDSYHTVWFELHEELIQAVGLTRDEAAKSGDAQ

4ci6B

0.12

0.11

1.00

0.76

MUSTER

LDMGVVLSDLDTMLVA-LDKAEREGGVDKDQLKSFNSLILKTYSVIGAYILSIVEPSLQRIQKHLDQTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSFRLAEAKVTLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYAIHRQMMAAHAAITLQEVSEFTDDMRNFTAD

4ke2A

0.09

0.98

0.75

dPPAS

----MNIDPAARAAAAAAASKAAVTAADAAAAAATIAASAASVAAATAADDAAASIATINAASAAAKSIAAAAAMAAKDTAAAAASAAAAAVASAAKALETINVKAAYAAATTANTAAAAAAATATTAAAAAAAKATIDNAAAAKAAAVATAVSDAAATAATAAAVAAATLEAAAAKAAATAVSAAAAAAAAAIAFAAAP-

3g3zA

0.14

0.07

0.52

0.83

wdPPAS

LNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGLSLTETGKAYAAPLTESAQEFSDKVFATFGDKRTTRLFADLDALAEVEKTISENK------------------------------------------------------------------------------------------------

4ci6B

0.12

0.11

0.98

0.73

wMUSTER

LDMGVVLSDLDTMLVA-LDKAEREGGVDKDQLKSFNSLILKTYSVIGAYILSIVEPSLQRIQKHLD---QTHSFSDIGSLMRAHKHLETLLEVLVTLSQQGQPVSSETYSAEAKVTLSQQLNTLQQQQESAKAQLSILINRSGSWADVARQSLQRFDSTRPVVKFGTEQYAIHRQMMAAHAAITLQEVSEFTDDMRNFTAD

1yg2A

0.15

0.11

0.77

0.93

wPPAS

L-PHVILTVLSTRG---TKEFSASIGASHQQVYRELNKMGEQGLVTCVLEVSITQAGRSALGEWFDQPTAHPT-------------VRDEFSAKLMACSVQS-----------AEPYRLQLAELVEESRKLVAHYQEIEAAYYA-----PAVLDKQQRLERLTLRR----LVRQAWIQWADEVLAEL---NAMA-------

2f5cA

0.12

0.08

0.66

0.98

dPPAS2

DYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLEKYRGLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEE------KIYNDVEGIEHHL-----------SWNSIDRIGDLVQYFEED----DARKKDLKSIQKKTEHHNQ-----------------------------------------------

5cwnA

0.12

0.11

0.99

0.89

PPAS

MDPEEILERAKES--LERAREASERGDEEEFRKAAEKALELAKRLVEQAKKEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVLEAAKVALRVAELAAKNGDKEVFKKAAESALEVAKRLVEVASKEGDPELVEEAAKVAEEVRKAKKQGDEEVYEKARETAREVKEELKRVREEK

4ijaA1

0.17

0.12

0.72

1.24

Env-PPAS

MNEKRVLREIYNHHNISRTQISKNLEINKATISSILNKLKYKSLVNEVGG------GRKPI--LLK--------------------VNHLYGYFIS-LDLTY----SS--------VEVMYNYFDGN---VIKHESYDLPKVSSILSIIKKHIDIQEKLDTYNVSIHVVDNEQHVTISIAKKIKEITNV------------

2x1gF

0.08

0.98

0.71

MUSTER

RVWDAEAYSNMNRAVKCVGTWIKNIGYTIEGCVTITAVLLEVVHYWPCIHGCMTADENELAESCLKTMVNIIIQPDCHNYPKTAFVLIKMFLDSLSEITK-TEWKRENDNEDIIVHIYMLFVSSVERHSTLLLSGITADPELSILVHRIVQEILHCTDKPG---IYPVEESCSTMALAFWYMLQDEVFAHKCWEYIKPLYA

5cwqA

0.12

0.99

0.70

dPPAS

RLQEARKRSEEARERGDLKELAEALIEEARAVQELARVACERGNSEEAERASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNSEEAE--RASEKAQRVLEEARKVSEEAREQGDDEVLALALIAIALAVLALAEVACCRGNKEEAERAYEDARRVEEEARKVKESAEEQGDSEVKRLAEEAE

(a)	Iden1 is the number of template residues identical to query divided by number of aligned residues.
(b)	Iden2 is the number of template residues identical to query divided by query sequence length.
(c)	Cov is equal the number of aligned template residues divided by query sequence length.
(d)	Norm. Zscore is the normalized Z-score of the threading alignments. A Normalized Z-score >1 means a good alignment.
(e)	Download Align. list the threading program used to identify the template provide the 3D structure of aligned regions of threading templates.

Top 5 final models predicted by I-TASSER

(For each target, I-TASSER simulations generate a large ensemble of structural conformations, called decoys. To select the final models, I-TASSER uses the SPICKER program to cluster all the decoys based on the pair-wise structure similarity, and reports up to five models which corresponds to the five largest structure clusters. The confidence of each model is quantitatively measured by C-score that is calculated based on the significance of threading template alignments and the convergence parameters of the structure assembly simulations. C-score is typically in the range of [-5, 2], where a C-score of higher value signifies a model with a high confidence and vice-versa. TM-score and RMSD are estimated based on C-score and protein length following the correlation observed between these qualities. Since the top 5 models are ranked by the cluster size, it is possible that the lower-rank models have a higher C-score in rare cases. Although the first model has a better quality in most cases, it is also possible that the lower-rank models have a better quality than the higher-rank models as seen in our benchmark tests. If the I-TASSER simulations converge, it is possible to have less than 5 clusters generated. This is usually an indication that the models have a good quality because of the converged simulations.)

More about C-score

Local structure accuracy of first model

Download Model 1

C-score=-3.26

Estimated TM-score = 0.35±0.12

Estimated RMSD = 13.0±4.2Å

Download Model 2

C-score=-2.09

Download Model 3

C-score=-2.40

Download Model 4

C-score=-3.22

Download Model 5

C-score=-3.45

Proteins structureally close to the target in PDB (as identified by TM-align

(After the structure assembly simulation, I-TASSER uses the TM-align structural alignment program to match the first I-TASSER model to all structures in the PDB library. This section reports the top 10 proteins from the PDB that have the closest structural similarity, i.e. the highest TM-score, to the predicted I-TASSER model. Due to the structural similarity, these proteins often have similar function to the target. However, users are encouraged to use the data in the next section 'Predicted function using COACH' to infer the function of the target protein, since COACH has been extensively trained to derive biological functions from multi-source of sequence and structure features which has on average a higher accuracy than the function annotations derived only from the global structure comparison.)

Top 10 Identified stuctural analogs in PDB

Rank	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov
1	3rkoN	0.554	5.12	0.040	0.881
2	4kf7A	0.548	5.37	0.098	0.915
3	5t8vA	0.533	4.66	0.072	0.806
4	3s4wB3	0.532	4.81	0.091	0.831
5	3rkoL	0.532	5.33	0.061	0.881
6	3s4wA3	0.529	4.85	0.114	0.826
7	4he8L	0.529	5.15	0.070	0.861
8	5cwmA	0.528	4.91	0.102	0.851
9	2pftA	0.526	4.91	0.110	0.806
10	4he8N	0.525	5.09	0.047	0.836

(a)	Query structure is shown in cartoon, while the structural analog is displayed using backbone trace.
(b)	Ranking of proteins is based on TM-score of the structural alignment between the query structure and known structures in the PDB library.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of the alignment by TM-align and is equal to the number of structurally aligned residues divided by length of the query protein.

Predicted function using COACH

(This section reports biological annotations of the target protein by COACH based on the I-TASSER structure prediction. COACH is a meta-server approach that combines multiple function annotation results from the COFACTOR, TM-SITE and S-SITE programs.)

Ligand binding sites

Rank	C-score	Cluster size	PDB Hit	Lig Name	Download Complex	Ligand Binding Site Residues
1	0.08	4	4fe1F	CLA	Rep, Mult	179,183
2	0.06	3	2fjcB	FE	Rep, Mult	164,173,180
3	0.06	3	4amjB	2CV	Rep, Mult	153,180,183,190
4	0.06	3	4toaA	FE2	Rep, Mult	178,182
5	0.04	2	3rkoL	LFA	Rep, Mult	149,152,153,183
6	0.04	2	1ta9A	ZN	Rep, Mult	28,108,125
7	0.02	1	1g6iA	DMJ	Rep, Mult	121,122,175,178
8	0.02	1	2g38B	MN	Rep, Mult	188,191,192
9	0.02	1	2wieA	CVM	Rep, Mult	131,135
10	0.02	1	3a9qG	CA	Rep, Mult	170,174
11	0.02	1	3gs30	III	Rep, Mult	121,122,125,128,129,132,136,142,147,150
12	0.02	1	3dugA	ZN	Rep, Mult	101,145,173
13	0.02	1	1b8dA	PEB	Rep, Mult	4,8
14	0.02	1	1icrA	NIO	Rep, Mult	178,188

	Download the all possible binding ligands and detailed prediction summary.
	Download the templates clustering results.
(a)	C-score is the confidence score of the prediction. C-score ranges [0-1], where a higher score indicates a more reliable prediction.
(b)	Cluster size is the total number of templates in a cluster.
(c)	Lig Name is name of possible binding ligand. Click the name to view its information in the BioLiP database.
(d)	Rep is a single complex structure with the most representative ligand in the cluster, i.e., the one listed in the Lig Name column. Mult is the complex structures with all potential binding ligands in the cluster.

Enzyme Commission (EC) numbers and active sites

Rank	Cscore^EC	PDB Hit	TM-score	RMSD^a	IDEN^a	Cov	EC Number	Active Site Residues
1	0.060	1f1sA	0.505	5.06	0.088	0.826	4.2.2.1	NA
2	0.060	2vn7A	0.478	5.27	0.050	0.796	3.2.1.3	4
3	0.060	1ii2A	0.467	5.25	0.048	0.741	4.1.1.49	NA
4	0.060	1dl2A	0.496	4.89	0.101	0.781	3.2.1.113	11
5	0.060	2ri9B	0.501	4.95	0.078	0.786	3.2.1.113	NA
6	0.060	1hcuB	0.507	4.87	0.059	0.796	3.2.1.113	15
7	0.060	1cleA	0.442	5.54	0.076	0.766	3.1.1.3	NA
8	0.060	1gaiA	0.480	5.25	0.045	0.806	3.2.1.3	181
9	0.060	1rw9A	0.495	5.32	0.064	0.831	4.2.2.5	NA
10	0.060	2pfdB	0.475	4.85	0.077	0.741	2.1.2.5,4.3.1.4	12
11	0.060	1yggA	0.415	5.30	0.045	0.697	4.1.1.49	NA
12	0.060	1w6jA	0.449	5.83	0.041	0.816	5.4.99.7	NA
13	0.060	1xjjA	0.445	5.35	0.084	0.726	1.17.4.1	44
14	0.060	2zbkA	0.462	4.61	0.069	0.692	5.99.1.3	17,31,36,51,93
15	0.060	2vn4A	0.474	5.25	0.061	0.801	3.2.1.3	178
16	0.060	2q1fA	0.465	5.21	0.067	0.781	4.2.2.21	NA
17	0.060	1hn0A	0.463	5.53	0.059	0.811	4.2.2.20	NA
18	0.060	3dsiA	0.448	5.17	0.045	0.721	4.2.1.92	146,187
19	0.060	1kktA	0.503	4.97	0.083	0.791	3.2.1.113	NA

(a)	Cscore^EC is the confidence score for the EC number prediction. Cscore^EC values range in between [0-1]; where a higher score indicates a more reliable EC number prediction.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.

Gene Ontology (GO) terms

Rank	Cscore^GO	TM-score	RMSD^a	IDEN^a	Cov	PDB Hit	Associated GO Terms
Homologous GO templates in PDB
0	0.07	0.526	5.09	0.05	0.83	4he8I	GO:0005886 GO:0006810 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0050136 GO:0055114
1	0.07	0.528	5.16	0.07	0.86	4he8F	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
2	0.07	0.548	5.37	0.10	0.92	4kf7A	GO:0005643 GO:0006406 GO:0006606 GO:0006999 GO:0017056 GO:0031990 GO:0044611
3	0.07	0.532	4.81	0.09	0.83	3s4wB	GO:0000793 GO:0005634 GO:0005730 GO:0005737 GO:0006281 GO:0006974 GO:0007049 GO:0007129 GO:0007275 GO:0007276 GO:0010332 GO:0034599 GO:0045589 GO:0048854 GO:0050727 GO:0051090 GO:0070182 GO:0097150 GO:2000348
4	0.07	0.451	4.30	0.05	0.67	4he8G	GO:0005886 GO:0008137 GO:0016020 GO:0016021 GO:0016491 GO:0042773 GO:0048038 GO:0055114
5	0.06	0.377	5.62	0.04	0.66	1k9xA	GO:0004180 GO:0004181 GO:0006508 GO:0008233 GO:0008237 GO:0016787 GO:0046872 GO:0050897
6	0.06	0.408	5.31	0.06	0.67	4f7rD	GO:0019904
7	0.06	0.361	5.60	0.08	0.61	1nfgA	GO:0005737 GO:0016787 GO:0016810 GO:0046872
8	0.06	0.363	4.72	0.05	0.55	4wnlC	GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0005789 GO:0005934 GO:0006810 GO:0007533 GO:0008289 GO:0008298 GO:0051028
9	0.06	0.356	5.40	0.06	0.60	3nurA	GO:0016787
10	0.06	0.354	5.50	0.04	0.62	4dozA	GO:0000166 GO:0003723 GO:0005737 GO:0046872 GO:0051607
11	0.06	0.286	5.93	0.03	0.53	5ahoA	GO:0000075 GO:0000723 GO:0000781 GO:0000784 GO:0003684 GO:0004518 GO:0004527 GO:0005634 GO:0005694 GO:0005737 GO:0005813 GO:0005815 GO:0005856 GO:0006281 GO:0006303 GO:0006974 GO:0008409 GO:0016787 GO:0031627 GO:0031848 GO:0031860 GO:0035312 GO:0036297 GO:0090305
12	0.06	0.339	4.21	0.07	0.48	1xlyB	GO:0003723 GO:0003729 GO:0005634 GO:0005737 GO:0005789 GO:0005934 GO:0006810 GO:0007533 GO:0008289 GO:0008298 GO:0051028
13	0.06	0.299	5.08	0.09	0.48	2cjwA	GO:0000166 GO:0000287 GO:0003924 GO:0005516 GO:0005525 GO:0005634 GO:0005886 GO:0006955 GO:0007067 GO:0007165 GO:0007166 GO:0007264 GO:0009898 GO:0016020 GO:0019003 GO:0030496 GO:0051233 GO:0051276 GO:0051310 GO:0072686
14	0.06	0.313	5.07	0.05	0.49	1z5xU
15	0.06	0.326	5.73	0.05	0.57	4q0mA	GO:0004067 GO:0006520
16	0.06	0.290	5.28	0.05	0.48	1p2xA	GO:0000281 GO:0000917 GO:0003779 GO:0005096 GO:0005516 GO:0005634 GO:0005635 GO:0005737 GO:0005816 GO:0005826 GO:0005856 GO:0007049 GO:0007165 GO:0007264 GO:0043087 GO:0043547 GO:0044732 GO:0051301 GO:0071341 GO:0071574 GO:1902405 GO:1903475 GO:1903477 GO:1903478 GO:1903479
17	0.06	0.336	4.79	0.05	0.51	3llvA	GO:0003676 GO:0006813
18	0.06	0.335	5.87	0.08	0.61	4mlcA	GO:0006865

Consensus prediction of GO terms

Molecular Function	GO:0050136	GO:0048037
GO-Score	0.37	0.37
Biological Processes	GO:0022904	GO:0006119
GO-Score	0.37	0.37
Cellular Component	GO:0071944
GO-Score	0.37

(a)	Cscore^GO is a combined measure for evaluating global and local similarity between query and template protein. It's range is [0-1] and higher values indicate more confident predictions.
(b)	TM-score is a measure of global structural similarity between query and template protein.
(c)	RMSD^a is the RMSD between residues that are structurally aligned by TM-align.
(d)	IDEN^a is the percentage sequence identity in the structurally aligned region.
(e)	Cov represents the coverage of global structural alignment and is equal to the number of structurally aligned residues divided by length of the query protein.
(f)	The second table shows a consensus GO terms amongst the top scoring templates. The GO-Score associated with each prediction is defined as the average weight of the GO term, where the weights are assigned based on Cscore^GO of the template.

[Click on result.tar.bz2 to download the tarball file including all modelling results listed on this page]

Please cite the following articles when you use the I-TASSER server:
1.	J Yang, R Yan, A Roy, D Xu, J Poisson, Y Zhang. The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12: 7-8, 2015.
2.	J Yang, Y Zhang. I-TASSER server: new development for protein structure and function predictions, Nucleic Acids Research, 43: W174-W181, 2015.
3.	A Roy, A Kucukural, Y Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, 5: 725-738, 2010.
4.	Y Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40, 2008.